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- PDB-1pwc: penicilloyl acyl enzyme complex of the Streptomyces R61 DD-peptid... -

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Basic information

Entry
Database: PDB / ID: 1pwc
Titlepenicilloyl acyl enzyme complex of the Streptomyces R61 DD-peptidase with penicillin G
ComponentsD-alanyl-D-alanine carboxypeptidase
KeywordsHYDROLASE / BETA-LACTAM / ANTIBIOTICS / PENICILLIN BINDING PROTEIN / ENZYME / PEPTIDOGLYCAN
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / extracellular region
Similarity search - Function
: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
OPEN FORM - PENICILLIN G / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.1 Å
AuthorsSilvaggi, N.R. / Josephine, H.R. / Pratt, R.F. / Kelly, J.A.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Crystal structures of complexes between the R61 DD-peptidase and peptidoglycan-mimetic beta-lactams: a non-covalent complex with a "perfect penicillin"
Authors: Silvaggi, N.R. / Josephine, H.R. / Kuzin, A.P. / Nagarajan, R. / Pratt, R.F. / Kelly, J.A.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Structures of Two Kinetic Intermediates Reveal Species Specificity of Penicillin-Binding Proteins
Authors: Mcdonough, M.A. / Anderson, J.W. / Silvaggi, N.R. / Pratt, R.F. / Knox, J.R. / Kelly, J.A.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: A 1.2-A Snapshot of the Final Step of Bacterial Cell Wall Biosynthesis
Authors: Lee, W. / Mcdonough, M.A. / Kotra, L. / Li, Z.H. / Silvaggi, N.R. / Takeda, Y. / Kelly, J.A. / Mobashery, S.
#3: Journal: J.Mol.Biol. / Year: 1995
Title: The Refined Crystallographic Structure of a Dd-Peptidase Penicillin-Target Enzyme at 1.6 A Resolution
Authors: Kelly, J.A. / Kuzin, A.P.
History
DepositionJul 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-alanyl-D-alanine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7592
Polymers37,4231
Non-polymers3361
Water9,134507
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.900, 66.700, 99.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D-alanyl-D-alanine carboxypeptidase / DD-peptidase / DD-carboxypeptidase


Mass: 37422.574 Da / Num. of mol.: 1 / Fragment: DD-PEPTIDASE / Source method: isolated from a natural source / Source: (natural) Streptomyces sp. (bacteria) / Strain: R61
References: UniProt: P15555, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-PNM / OPEN FORM - PENICILLIN G


Mass: 336.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N2O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20% PEG 8000, 50mM Sodium Phosphate, pH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Apr 14, 2003 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. all: 131101 / Num. obs: 131101 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.4
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 3.5 / Num. unique all: 8799 / % possible all: 64.1

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3PTE

3pte


Resolution: 1.1→10 Å / Num. parameters: 28737 / Num. restraintsaints: 0 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.026.
RfactorNum. reflection% reflectionSelection details
Rfree0.1479 6469 5.1 %RANDOM
Rwork0.1201 ---
all0.1243 127466 --
obs0.1201 127466 92.6 %-
Refine analyzeLuzzati coordinate error obs: 0.07 Å / Num. disordered residues: 18 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3112.5
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 23 507 3132
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.029
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.032
X-RAY DIFFRACTIONs_zero_chiral_vol0.084
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.088
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.039
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.036
X-RAY DIFFRACTIONs_approx_iso_adps0.094

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